NEW YORK, Sept 27 (Reuters) - A unit of AmerisourceBergen Corp, one of the largest U.S. drug wholesalers, on Wednesday pleaded guilty to selling pre-filled syringes of cancer drugs prepared in ways that violated federal rules, agreeing to pay penalties of $260 million.

AmerisourceBergen Specialty Group pleaded guilty to selling misbranded drugs in violation of the federal Food, Drug and Cosmetic Act, a misdemeanor, before U.S. District Judge Nina Gershon in Brooklyn.

AmerisourceBergen disclosed the plea agreement and expected payment in August. The company also said it may still face related civil claims by the government.

In a court document filed Wednesday, AmerisourceBergen admitted its now-defunct subsidiary, Medical Initiatives Inc, packaged syringes of cancer drugs at an Alabama facility that was not registered with the U.S. Food and Drug Administration, as required by federal law.

The company admitted that Medical Initiatives illegally dispensed syringes based on order forms that were not prescriptions signed by medical practitioners. It also said it submitted syringes on behalf of single patients in excess of safe doses.

AmerisourceBergen said the violations occurred from 2005 until 2014.

In a criminal information unsealed Wednesday, prosecutors also charged that Medical Initiatives prepared syringes by pooling drugs sold in glass vials that were meant for a single use, and did not maintain a sterile environment in its facility, resulting in contamination in some syringes.

AmerisourceBergen said it remained free to contest claims in the criminal information to which it did not plead guilty, in future legal proceedings.

The U.S. Attorney’s Office in Brooklyn, which brought the criminal charge, also intends to pursue civil claims under the False Claims Act, the company said in August. Under the act, the government can recover taxpayer money paid out based on fraudulent claims.

The company said at the time that while it was in talks to resolve the civil claims, “significant disagreements” existed between both sides, and it was unclear if a settlement could be reached.

John Marzulli, a spokesman for the U.S. Attorney’s Office, declined to comment on whether the office will bring a civil lawsuit.

Shares of AmerisourceBergen were unchanged at $82. (Additional reporting by Nate Raymond in Boston; Editing by Chizu Nomiyama and Jeffrey Benkoe)